Drosophila Evolution over Space and Time (DEST) - a new population genomics resource

Martin Kapun*, Joaquin C B Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P García Guerreiro, Sònia Casillas, Dorcas J Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S Onder, Jessica K Abbott, Stephen W Schaeffer, Subhash RajpurohitEmily L Behrman, Mads F Schou, Thomas J S Merritt, Brian P Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana V Serga, Daniel K Fabian, Kelly A Dyer, Christopher W Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J Buendía-Ruíz, M Josefa Gómez-Julián, M Luisa Espinosa-Jimenez, Francisco D Gallardo-Jiménez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horváth, Darren J Obbard, Elena Pasyukova, Vladimir E Alatortsev, Cristina P Vieira, Jorge Vieira, J Roberto Torres, Iryna Kozeretska, Oleksandr M Maistrenko, Catherine Montchamp-Moreau, Dmitry V Mukha, Heather E Machado, Keric Lamb, Tânia Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov*, Paul Schmidt*, Josefa Gonzalez*, Thomas Flatt*, Alan O Bergland*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)
4 Downloads (Pure)


Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
Original languageEnglish
Article numbermsab259
Pages (from-to)5782-5805
Number of pages24
JournalMolecular Biology and Evolution
Issue number12
Early online date1 Sept 2021
Publication statusPublished - 1 Dec 2021


  • Demography
  • Population genomics
  • Drosophila melanogaster
  • SNPs
  • Evolution
  • Adaptation


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